Detection of Bacterial and Viral Pathogens Using Photonic Point-of-Care Devices

Rapid and sensitive detection of Staphylococcus aureus using a THz metamaterial biosensor based on aptamer-functionalized Fe3O4@Au nanocomposites

Staphylococcus aureus (S. aureus) poses a serious threat to global public health, necessitating the establishment of rapid and simple tools for its accurate identification. Herein, we developed a terahertz (THz) metamaterial biosensor based on aptamer-functionalized Fe3O4@Au nanocomposites for quantitative S. aureus assays in different clinical samples. Fe3O4@Au@Cys@Apt has the dual advantages of magnetism and a high refractive index in the THz range and was used to rapidly separate and enrich target bacteria in a complex environmental solution. Furthermore, conjugation to the nanocomposites significantly increased the resonance frequency shift of the THz metamaterial after target loading. Our results showed that the shifts in the metamaterial resonance frequency were linearly related to S. aureus concentrations ranging from 1.0 × 103 to 1.0 × 107 CFU/mL, with a detection limit of 4.78 × 102 CFU/mL. The biosensor was further applied to S. aureus detection in spiked human urine and blood with satisfactory recoveries (82.4-109.6%). Our approach also demonstrated strong concordance with traditional plate counting (R2 = 0.99306) while significantly lowering the analysis time from 24 h to <1 h. In conclusion, the proposed biosensor can not only perform culture-free and extraction-free detection of target bacteria but can also be easily extended to the determination of other pathogenic bacteria, rendering it suitable for various bacteria-related disease diagnoses.

Fast detection of bacterial gut pathogens on miniaturized devices: an overview

INTRODUCTION

Gut microbes pose challenges like colon inflammation, deadly diarrhea, antimicrobial resistance dissemination, and chronic disease onset. Development of early, rapid and specific diagnosis tools is essential for improving infection control. Point-of-care testing (POCT) systems offer rapid, sensitive, low-cost and sample-to-answer methods for microbe detection from various clinical and environmental samples, bringing the advantages of portability, automation, and simple operation.

AREAS COVERED

Rapid detection of gut microbes can be done using a wide array of techniques including biosensors, immunological assays, electrochemical impedance spectroscopy, mass spectrometry and molecular biology. Inclusion of Internet of Things, machine learning, and smartphone-based point-of-care applications is an important aspect of POCT. In this review, the authors discuss various fast diagnostic platforms for gut pathogens and their main challenges.

EXPERT OPINION

Developing effective assays for microbe detection can be complex. Assay design must consider factors like target selection, real-time and multiplex detection, sample type, reagent stability and storage, primer/probe design, and optimizing reaction conditions for accuracy and sensitivity. Mitigating these challenges requires interdisciplinary collaboration among scientists, clinicians, engineers, and industry partners. Future efforts are essential to enhance sensitivity, specificity, and versatility of POCT systems for gut microbe detection and quantification, advancing infectious disease diagnostics and management.

Research advances in microfluidic collection and detection of virus, bacterial, and fungal bioaerosols

Bioaerosols are airborne suspensions of fine solid or liquid particles containing biological substances such as viruses, bacteria, cellular debris, fungal spores, mycelium, and byproducts of microbial metabolism. The global Coronavirus disease 2019 (COVID-19) pandemic and the previous emergence of severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and influenza have increased the need for reliable and effective monitoring tools for bioaerosols. Bioaerosol collection and detection have aroused considerable attention. Current bioaerosol sampling and detection techniques suffer from long response time, low sensitivity, and high costs, and these drawbacks have forced the development of novel monitoring strategies. Microfluidic technique is considered a breakthrough for high performance analysis of bioaerosols. In recent years, several emerging methods based on microfluidics have been developed and reported for collection and detection of bioaerosols. The unique advantages of microfluidic technique have enabled the integration of bioaerosol collection and detection, which has a higher efficiency over conventional methods. This review focused on the research progress of bioaerosol collection and detection methods based on microfluidic techniques, with special attention on virus aerosols and bacterial aerosols. Different from the existing reviews, this work took a unique perspective of the targets to be collected and detected in bioaerosols, which would provide a direct index of bioaerosol categories readers may be interested in. We also discussed integrated microfluidic monitoring system for bioaerosols. Additionally, the application of bioaerosol detection in biomedicine was presented. Finally, the current challenges in the field of bioaerosol monitoring are presented and an outlook given of future developments.

Advances in the detection and diagnosis of tuberculosis using optical-based devices

Tuberculosis (TB), a bacterial infection caused by Mycobacterium tuberculosis, is highly contagious and can lead to severe health complications if left untreated. This review article discusses the importance of early detection and treatment and its global incidence and epidemiology, emphasizing its impact on vulnerable populations and its role as a major cause of death worldwide. Furthermore, it highlights the challenges faced with diagnosing TB. To overcome these challenges, point-of-care devices have emerged as promising tools for rapid and accurate TB detection. These include devices such as nucleic acid amplification tests (NAATs), lateral flow assays (LFAs), and microfluidic-based assays, which offer advantages such as rapid results, portability, and the ability to detect drug-resistant strains. Optical-based devices, such as photonic micro-ring sensors, silicon platform-based sensors, plasmonic-based platforms, microfluidics, and smartphone imaging, are some of the highlighted optical-based devices with the potential to detect TB. These devices can detect TB in sputum samples with high sensitivity and specificity. Optical-based diagnostic devices have the potential to offer the advantages of detecting low concentrations of target molecules and being adaptable to detect multiple targets simultaneously. Using these devices in a clinical setting makes them suitable for their application in improving access to diagnostic testing that enables earlier detection and treatment of TB. Furthermore, these devices would improve TB's global health issue, which requires comprehensive research, prevention, and treatment efforts.

Polyethylene Glycol-Mediated Directional Conjugation of Biological Molecules for Enhanced Immunoassays at the Point-of-Care

Rapid and reliable point-of-care (POC) diagnostic tests can have a significant impact on global health. One of the most common approaches for developing POC systems is the use of target-specific biomolecules. However, the conjugation of biomolecules can result in decreased activity, which may compromise the analytical performance and accuracy of the developed systems. To overcome this challenge, we present a polymer-based cross-linking protocol for controlled and directed conjugation of biological molecules. Our protocol utilizes a bifunctional thiol-polyethylene glycol (PEG)-hydrazide polymer to enable site-directed conjugation of IgG antibodies to the surface of screen-printed metal electrodes. The metal surface of the electrodes is first modified with thiolated PEG molecules, leaving the hydrazide groups available to react with the aldehyde group in the Fc fragments of the oxidized IgG antibodies. Using anti-Klebsiella pneumoniae carbapenemase-2 (KPC-2) antibody as a model antibody used for antimicrobial resistance (AMR) testing, our results demonstrate a ~10-fold increase in antibody coupling compared with the standard N-hydroxysuccinimide (NHS)-based conjugation chemistry and effective capture (>94%) of the target KPC-2 enzyme antigen on the surface of modified electrodes. This straightforward and easy-to-perform strategy of site-directed antibody conjugation can be engineered for coupling other protein- and non-protein-based biological molecules commonly used in POC testing and development, thus enhancing the potential for improved diagnostic accuracy and performance.

Biosensors Based on Inorganic Composite Fluorescent Hydrogels

Fluorescent hydrogels are promising candidate materials for portable biosensors to be used in point-of-care diagnosis because (1) they have a greater capacity for binding organic molecules than immunochromatographic test systems, determined by the immobilization of affinity labels within the three-dimensional hydrogel structure; (2) fluorescent detection is more sensitive than the colorimetric detection of gold nanoparticles or stained latex microparticles; (3) the properties of the gel matrix can be finely tuned for better compatibility and detection of different analytes; and (4) hydrogel biosensors can be made to be reusable and suitable for studying dynamic processes in real time. Water-soluble fluorescent nanocrystals are widely used for in vitro and in vivo biological imaging due to their unique optical properties, and hydrogels based on these allow the preservation of these properties in bulk composite macrostructures. Here we review the techniques for obtaining analyte-sensitive fluorescent hydrogels based on nanocrystals, the main methods used for detecting the fluorescent signal changes, and the approaches to the formation of inorganic fluorescent hydrogels via sol-gel phase transition using surface ligands of the nanocrystals.

Fluorescence-Based Portable Assays for Detection of Biological and Chemical Analytes

Fluorescence-based detection techniques are part of an ever-expanding field and are widely used in biomedical and environmental research as a biosensing tool. These techniques have high sensitivity, selectivity, and a short response time, making them a valuable tool for developing bio-chemical assays. The endpoint of these assays is defined by changes in fluorescence signal, in terms of its intensity, lifetime, and/or shift in spectrum, which is monitored using readout devices such as microscopes, fluorometers, and cytometers. However, these devices are often bulky, expensive, and require supervision to operate, which makes them inaccessible in resource-limited settings. To address these issues, significant effort has been directed towards integrating fluorescence-based assays into miniature platforms based on papers, hydrogels, and microfluidic devices, and to couple these assays with portable readout devices like smartphones and wearable optical sensors, thereby enabling point-of-care detection of bio-chemical analytes. This review highlights some of the recently developed portable fluorescence-based assays by discussing the design of fluorescent sensor molecules, their sensing strategy, and the fabrication of point-of-care devices.

An Overview of the Public Health Challenges in Diagnosing and Controlling Human Foodborne Pathogens

Pathogens found in food are believed to be the leading cause of foodborne illnesses; and they are considered a serious problem with global ramifications. During the last few decades, a lot of attention has been paid to determining the microorganisms that cause foodborne illnesses and developing new methods to identify them. Foodborne pathogen identification technologies have evolved rapidly over the last few decades, with the newer technologies focusing on immunoassays, genome-wide approaches, biosensors, and mass spectrometry as the primary methods of identification. Bacteriophages (phages), probiotics and prebiotics were known to have the ability to combat bacterial diseases since the turn of the 20th century. A primary focus of phage use was the development of medical therapies; however, its use quickly expanded to other applications in biotechnology and industry. A similar argument can be made with regards to the food safety industry, as diseases directly endanger the health of customers. Recently, a lot of attention has been paid to bacteriophages, probiotics and prebiotics most likely due to the exhaustion of traditional antibiotics. Reviewing a variety of current quick identification techniques is the purpose of this study. Using these techniques, we are able to quickly identify foodborne pathogenic bacteria, which forms the basis for future research advances. A review of recent studies on the use of phages, probiotics and prebiotics as a means of combating significant foodborne diseases is also presented. Furthermore, we discussed the advantages of using phages as well as the challenges they face, especially given their prevalent application in food safety.

Fast Track Diagnostic Tools for Clinical Management of Sepsis: Paradigm Shift from Conventional to Advanced Methods

Sepsis is one of the deadliest disorders in the new century due to specific limitations in early and differential diagnosis. Moreover, antimicrobial resistance (AMR) is becoming the dominant threat to human health globally. The only way to encounter the spread and emergence of AMR is through the active detection and identification of the pathogen along with the quantification of resistance. For better management of such disease, there is an essential requirement to approach many suitable diagnostic techniques for the proper administration of antibiotics and elimination of these infectious diseases. The current method employed for the diagnosis of sepsis relies on the conventional culture of blood suspected infection. However, this method is more time consuming and generates results that are false negative in the case of antibiotic pretreated samples as well as slow-growing microbes. In comparison to the conventional method, modern methods are capable of analyzing blood samples, obtaining accurate results from the suspicious patient of sepsis, and giving all the necessary information to identify the pathogens as well as AMR in a short period. The present review is intended to highlight the culture shift from conventional to modern and advanced technologies including their limitations for the proper and prompt diagnosing of bloodstream infections and AMR detection.

Electrochemical Aptasensor for the Detection of the Key Virulence Factor YadA of Yersinia enterocolitica

New point-of-care (POC) diagnosis of bacterial infections are imperative to overcome the deficiencies of conventional methods, such as culture and molecular methods. In this study, we identified new aptamers that bind to the virulence factor Yersinia adhesin A (YadA) of Yersinia enterocolitica using cell-systematic evolution of ligands by exponential enrichment (cell-SELEX). Escherichia coli expressing YadA on the cell surface was used as a target cell. After eight cycles of selection, the final aptamer pool was sequenced by high throughput sequencing using the Illumina Novaseq platform. The sequencing data, analyzed using the Geneious software, was aligned, filtered and demultiplexed to obtain the key nucleotides possibly involved in the target binding. The most promising aptamer candidate, Apt1, bound specifically to YadA with a dissociation constant (Kd) of 11 nM. Apt1 was used to develop a simple electrochemical biosensor with a two-step, label-free design towards the detection of YadA. The sensor surface modifications and its ability to bind successfully and stably to YadA were confirmed by cyclic voltammetry, impedance spectroscopy and square wave voltammetry. The biosensor enabled the detection of YadA in a linear range between 7.0 × 104 and 7.0 × 107 CFU mL−1 and showed a square correlation coefficient >0.99. The standard deviation and the limit of detection was ~2.5% and 7.0 × 104 CFU mL−1, respectively. Overall, the results suggest that this novel biosensor incorporating Apt1 can potentially be used as a sensitive POC detection system to aid the diagnosis of Y. enterocolitica infections. Furthermore, this simple yet innovative approach could be replicated to select aptamers for other (bacterial) targets and to develop the corresponding biosensors for their detection.

Research progress on detection techniques for point-of-care testing of foodborne pathogens

The global burden of foodborne disease is enormous and foodborne pathogens are the leading cause of human illnesses. The detection of foodborne pathogenic bacteria has become a research hotspot in recent years. Rapid detection methods based on immunoassay, molecular biology, microfluidic chip, metabolism, biosensor, and mass spectrometry have developed rapidly and become the main methods for the detection of foodborne pathogens. This study reviewed a variety of rapid detection methods in recent years. The research advances are introduced based on the above technical methods for the rapid detection of foodborne pathogenic bacteria. The study also discusses the limitations of existing methods and their advantages and future development direction, to form an overall understanding of the detection methods, and for point-of-care testing (POCT) applications to accurately and rapidly diagnose and control diseases.

Automated detection of apoptotic versus nonapoptotic cell death using label-free computational microscopy

Identification of cell death mechanisms, particularly distinguishing between apoptotic versus nonapoptotic pathways, is of paramount importance for a wide range of applications related to cell signaling, interaction with pathogens, therapeutic processes, drug discovery, drug resistance, and even pathogenesis of diseases like cancers and neurogenerative disease among others. Here, we present a novel high-throughput method of identifying apoptotic versus necrotic versus other nonapoptotic cell death processes, based on lensless digital holography. This method relies on identification of the temporal changes in the morphological features of mammalian cells, which are unique to each cell death processes. Different cell death processes were induced by known cytotoxic agents. A deep learning-based approach was used to automatically classify the cell death mechanism (apoptotic vs necrotic vs nonapoptotic) with more than 93% accuracy. This label free approach can provide a low cost (<$250) alternative to some of the currently available high content imaging-based screening tools.

A comprehensive review on LED-induced fluorescence in diagnostic pathology

Sensitivity, specificity, mobility, and affordability are important criteria to consider for developing diagnostic instruments in common use. Fluorescence spectroscopy has been demonstrating substantial potential in the clinical diagnosis of diseases and evaluating the underlying causes of pathogenesis. A higher degree of device integration with appropriate sensitivity and reasonable cost would further boost the value of the fluorescence techniques in clinical diagnosis and aid in the reduction of healthcare expenses, which is a key economic concern in emerging markets. Light-emitting diodes (LEDs), which are inexpensive and smaller are attractive alternatives to conventional excitation sources in fluorescence spectroscopy, are gaining a lot of momentum in the development of affordable, compact analytical instruments of clinical relevance. The commercial availability of a broad range of LED wavelengths (255-4600 nm) has opened up new avenues for targeting a wide range of clinically significant molecules (both endogenous and exogenous), thereby diagnosing a range of clinical illnesses. As a result, we have specifically examined the uses of LED-induced fluorescence (LED-IF) in preclinical and clinical evaluations of pathological conditions, considering the present advancements in the field.

Development of Integrated Systems for On-Site Infection Detection

The modern healthcare system faces an unrelenting threat from microorganisms, as evidenced by global outbreaks of new viral diseases, emerging antimicrobial resistance, and the rising incidence of healthcare-associated infections (HAIs). An effective response to these threats requires rapid and accurate diagnostic tests that can identify causative pathogens at the point of care (POC). Such tests could eliminate diagnostic uncertainties, facilitating patient triaging, minimizing the empiric use of antimicrobial drugs, and enabling targeted treatments. Current standard methods, however, often fail to meet the needs of rapid diagnosis in POC settings. Culture-based assays entail long processing times and require specialized laboratory infrastructure; nucleic acid (NA) tests are often limited to centralized hospitals due to assay complexity and high costs. Here we discuss two new POC tests developed in our groups to enable the rapid diagnosis of infection. The first is nanoPCR that takes advantages of core-shell magnetoplasmonic nanoparticles (MPNs): (i) Au shell significantly accelerates thermocycling via volumetric, plasmonic light-to-heat conversion and (ii) a magnetic core enables sensitive in situ fluorescent detection via magnetic clearing. By adopting a Ferris wheel module, the system expedites multisamples in parallel with a minimal setup. When applied to COVID-19 diagnosis, nanoPCR detected SARS-CoV-2 RNA down to 3.2 copy/μL within 17 min. In particular, nanoPCR diagnostics accurately identified COVID-19 cases in clinical samples (n = 150), validating its clinical applicability. The second is a polarization anisotropy diagnostic (PAD) system that exploits the principle of fluorescence polarization (FP) as a detection modality. Fluorescent probes were designed to alter their molecular weight upon recognizing target NAs. This event modulates the probes' tumbling rate (Brownian motion), which leads to changes in FP. The approach is robust against environmental noise and benefits from the ratiometric nature of the signal readout. We applied PAD to detect clinically relevant HAI bacteria (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Staphylococcus aureus). The PAD assay demonstrated detection sensitivity down to the single bacterium level and determined both drug resistance and virulence status. In summary, these new tests have the potential to become powerful tools for rapid diagnosis in the infectious disease space. They do not require highly skilled personnel or labor-intensive analyses, and the assays are quick and cost-effective. These attributes will make nanoPCR and PAD well-aligned with a POC workflow to aid physicians to initiate prompt and informed patient treatment.

Conventional and microfluidic methods for airborne virus isolation and detection

With the COVID-19 pandemic, the threat of infectious diseases to public health and safety has become much more apparent. Viral, bacterial and fungal diseases have led to the loss of millions of lives, especially in the developing world. Diseases caused by airborne viruses like SARS-CoV-2 are difficult to control, as these viruses are easily transmissible and can circulate in the air for hours. To contain outbreaks of viruses such as SARS-CoV-2 and institute targeted precautions, it is important to detect them in air and understand how they infect their targets. Point-of-care (PoC) diagnostics and point-of-need (PoN) detection methods are necessary to rapidly test patient and environmental samples, so precautions can immediately be applied. Traditional benchtop detection methods such as ELISA, PCR and culture are not suitable for PoC and PoN monitoring, because they can take hours to days and require specialized equipment. Microfluidic devices can be made at low cost to perform such assays rapidly and at the PoN. They can also be integrated with air- and liquid-based sampling technologies to capture and analyze viruses from air and body fluids. Here, conventional and microfluidic virus detection methods are reviewed and compared. The use of air sampling devices to capture and concentrate viruses is discussed first, followed by a review of analysis methods such as immunoassays, RT-PCR and isothermal amplification in conventional and microfluidic platforms. This review provides an overview of the capabilities of microfluidics in virus handling and detection, which will be useful to infectious disease researchers, biomedical engineers, and public health agencies.

Roadmap on Universal Photonic Biosensors for Real-Time Detection of Emerging Pathogens

The COVID-19 pandemic has made it abundantly clear that the state-of-the-art biosensors may not be adequate for providing a tool for rapid mass testing and population screening in response to newly emerging pathogens. The main limitations of the conventional techniques are their dependency on virus-specific receptors and reagents that need to be custom-developed for each recently-emerged pathogen, the time required for this development as well as for sample preparation and detection, the need for biological amplification, which can increase false positive outcomes, and the cost and size of the necessary equipment. Thus, new platform technologies that can be readily modified as soon as new pathogens are detected, sequenced, and characterized are needed to enable rapid deployment and mass distribution of biosensors. This need can be addressed by the development of adaptive, multiplexed, and affordable sensing technologies that can avoid the conventional biological amplification step, make use of the optical and/or electrical signal amplification, and shorten both the preliminary development and the point-of-care testing time frames. We provide a comparative review of the existing and emergent photonic biosensing techniques by matching them to the above criteria and capabilities of preventing the spread of the next global pandemic.

Diagnosis of Herpes Simplex Virus: Laboratory and Point-of-Care Techniques

Herpes is a widespread viral infection caused by the herpes simplex virus (HSV) that has no permanent cure to date. There are two subtypes, HSV-1 and HSV-2, that are known to cause a variety of symptoms, ranging from acute to chronic. HSV is highly contagious and can be transmitted via any type of physical contact. Additionally, viral shedding can also happen from asymptomatic infections. Thus, early and accurate detection of HSV is needed to prevent the transmission of this infection. Herpes can be diagnosed in two ways, by either detecting the presence of the virus in lesions or the antibodies in the blood. Different detection techniques are available based on both laboratory and point of care (POC) devices. Laboratory techniques include different biochemical assays, microscopy, and nucleic acid amplification. In contrast, POC techniques include microfluidics-based tests that enable on-spot testing. Here, we aim to review the different diagnostic techniques, both laboratory-based and POC, their limits of detection, sensitivity, and specificity, as well as their advantages and disadvantages.

Diagnosis for COVID-19: current status and future prospects

Introduction: Coronavirus disease 2019 (COVID-19), a respiratory illness caused by novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), had its first detection in December 2019 in Wuhan (China) and spread across the world. In March 2020, the World Health Organization (WHO) declared COVID-19 a pandemic disease. The utilization of prompt and accurate molecular diagnosis of SARS-CoV-2 virus, isolating the infected patients, and treating them are the keys to managing this unprecedented pandemic. International travel acted as a catalyst for the widespread transmission of the virus.Areas covered: This review discusses phenotype, structural, and molecular evolution of recognition elements and primers, its detection in the laboratory, and at point of care. Further, market analysis of commercial products and their performance are also evaluated, providing new ways to confront the ongoing global public health emergency.Expert commentary: The outbreak for COVID-19 created mammoth chaos in the healthcare sector, and still, day by day, new epicenters for the outbreak are being reported. Emphasis should be placed on developing more effective, rapid, and early diagnostic devices. The testing laboratories should invest more in clinically relevant multiplexed and scalable detection tools to fight against a pandemic like this where massive demand for testing exists.